Job ID = 2590352 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T11:53:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T11:53:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 12,833,427 reads read : 25,666,854 reads written : 12,833,427 reads 0-length : 12,833,427 spots read : 12,697,064 reads read : 25,394,128 reads written : 12,697,064 reads 0-length : 12,697,064 spots read : 12,832,291 reads read : 25,664,582 reads written : 12,832,291 reads 0-length : 12,832,291 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:06 38362782 reads; of these: 38362782 (100.00%) were unpaired; of these: 1438875 (3.75%) aligned 0 times 30099477 (78.46%) aligned exactly 1 time 6824430 (17.79%) aligned >1 times 96.25% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6329183 / 36923907 = 0.1714 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 21:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 21:29:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:29:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 21:29:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:29:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 21:29:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:29:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:29:36: 1000000 INFO @ Mon, 12 Aug 2019 21:29:37: 1000000 INFO @ Mon, 12 Aug 2019 21:29:38: 1000000 INFO @ Mon, 12 Aug 2019 21:29:43: 2000000 INFO @ Mon, 12 Aug 2019 21:29:44: 2000000 INFO @ Mon, 12 Aug 2019 21:29:46: 2000000 INFO @ Mon, 12 Aug 2019 21:29:50: 3000000 INFO @ Mon, 12 Aug 2019 21:29:51: 3000000 INFO @ Mon, 12 Aug 2019 21:29:54: 3000000 INFO @ Mon, 12 Aug 2019 21:29:57: 4000000 INFO @ Mon, 12 Aug 2019 21:29:59: 4000000 INFO @ Mon, 12 Aug 2019 21:30:03: 4000000 INFO @ Mon, 12 Aug 2019 21:30:04: 5000000 INFO @ Mon, 12 Aug 2019 21:30:06: 5000000 INFO @ Mon, 12 Aug 2019 21:30:11: 5000000 INFO @ Mon, 12 Aug 2019 21:30:12: 6000000 INFO @ Mon, 12 Aug 2019 21:30:13: 6000000 INFO @ Mon, 12 Aug 2019 21:30:19: 7000000 INFO @ Mon, 12 Aug 2019 21:30:19: 6000000 INFO @ Mon, 12 Aug 2019 21:30:20: 7000000 INFO @ Mon, 12 Aug 2019 21:30:26: 8000000 INFO @ Mon, 12 Aug 2019 21:30:27: 7000000 INFO @ Mon, 12 Aug 2019 21:30:28: 8000000 INFO @ Mon, 12 Aug 2019 21:30:33: 9000000 INFO @ Mon, 12 Aug 2019 21:30:35: 9000000 INFO @ Mon, 12 Aug 2019 21:30:35: 8000000 INFO @ Mon, 12 Aug 2019 21:30:40: 10000000 INFO @ Mon, 12 Aug 2019 21:30:42: 10000000 INFO @ Mon, 12 Aug 2019 21:30:43: 9000000 INFO @ Mon, 12 Aug 2019 21:30:47: 11000000 INFO @ Mon, 12 Aug 2019 21:30:49: 11000000 INFO @ Mon, 12 Aug 2019 21:30:52: 10000000 INFO @ Mon, 12 Aug 2019 21:30:55: 12000000 INFO @ Mon, 12 Aug 2019 21:30:56: 12000000 INFO @ Mon, 12 Aug 2019 21:31:00: 11000000 INFO @ Mon, 12 Aug 2019 21:31:02: 13000000 INFO @ Mon, 12 Aug 2019 21:31:04: 13000000 INFO @ Mon, 12 Aug 2019 21:31:08: 12000000 INFO @ Mon, 12 Aug 2019 21:31:09: 14000000 INFO @ Mon, 12 Aug 2019 21:31:11: 14000000 INFO @ Mon, 12 Aug 2019 21:31:16: 13000000 INFO @ Mon, 12 Aug 2019 21:31:16: 15000000 INFO @ Mon, 12 Aug 2019 21:31:18: 15000000 INFO @ Mon, 12 Aug 2019 21:31:24: 16000000 INFO @ Mon, 12 Aug 2019 21:31:25: 14000000 INFO @ Mon, 12 Aug 2019 21:31:26: 16000000 INFO @ Mon, 12 Aug 2019 21:31:33: 17000000 INFO @ Mon, 12 Aug 2019 21:31:33: 17000000 INFO @ Mon, 12 Aug 2019 21:31:34: 15000000 INFO @ Mon, 12 Aug 2019 21:31:41: 18000000 INFO @ Mon, 12 Aug 2019 21:31:41: 18000000 INFO @ Mon, 12 Aug 2019 21:31:42: 16000000 INFO @ Mon, 12 Aug 2019 21:31:48: 19000000 INFO @ Mon, 12 Aug 2019 21:31:49: 19000000 INFO @ Mon, 12 Aug 2019 21:31:51: 17000000 INFO @ Mon, 12 Aug 2019 21:31:56: 20000000 INFO @ Mon, 12 Aug 2019 21:31:56: 20000000 INFO @ Mon, 12 Aug 2019 21:31:59: 18000000 INFO @ Mon, 12 Aug 2019 21:32:04: 21000000 INFO @ Mon, 12 Aug 2019 21:32:04: 21000000 INFO @ Mon, 12 Aug 2019 21:32:07: 19000000 INFO @ Mon, 12 Aug 2019 21:32:11: 22000000 INFO @ Mon, 12 Aug 2019 21:32:12: 22000000 INFO @ Mon, 12 Aug 2019 21:32:15: 20000000 INFO @ Mon, 12 Aug 2019 21:32:19: 23000000 INFO @ Mon, 12 Aug 2019 21:32:19: 23000000 INFO @ Mon, 12 Aug 2019 21:32:23: 21000000 INFO @ Mon, 12 Aug 2019 21:32:26: 24000000 INFO @ Mon, 12 Aug 2019 21:32:27: 24000000 INFO @ Mon, 12 Aug 2019 21:32:31: 22000000 INFO @ Mon, 12 Aug 2019 21:32:33: 25000000 INFO @ Mon, 12 Aug 2019 21:32:34: 25000000 INFO @ Mon, 12 Aug 2019 21:32:39: 23000000 INFO @ Mon, 12 Aug 2019 21:32:41: 26000000 INFO @ Mon, 12 Aug 2019 21:32:42: 26000000 INFO @ Mon, 12 Aug 2019 21:32:48: 24000000 INFO @ Mon, 12 Aug 2019 21:32:48: 27000000 INFO @ Mon, 12 Aug 2019 21:32:49: 27000000 INFO @ Mon, 12 Aug 2019 21:32:55: 28000000 INFO @ Mon, 12 Aug 2019 21:32:56: 28000000 INFO @ Mon, 12 Aug 2019 21:32:56: 25000000 INFO @ Mon, 12 Aug 2019 21:33:02: 29000000 INFO @ Mon, 12 Aug 2019 21:33:03: 29000000 INFO @ Mon, 12 Aug 2019 21:33:04: 26000000 INFO @ Mon, 12 Aug 2019 21:33:09: 30000000 INFO @ Mon, 12 Aug 2019 21:33:10: 30000000 INFO @ Mon, 12 Aug 2019 21:33:12: 27000000 INFO @ Mon, 12 Aug 2019 21:33:13: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:33:13: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:33:13: #1 total tags in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:33:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:33:14: #1 tags after filtering in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:33:14: #1 finished! INFO @ Mon, 12 Aug 2019 21:33:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:33:14: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:33:14: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:33:14: #1 total tags in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:33:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:33:15: #1 tags after filtering in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:33:15: #1 finished! INFO @ Mon, 12 Aug 2019 21:33:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:33:17: #2 number of paired peaks: 547 WARNING @ Mon, 12 Aug 2019 21:33:17: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Mon, 12 Aug 2019 21:33:17: start model_add_line... INFO @ Mon, 12 Aug 2019 21:33:17: start X-correlation... INFO @ Mon, 12 Aug 2019 21:33:17: end of X-cor INFO @ Mon, 12 Aug 2019 21:33:17: #2 finished! INFO @ Mon, 12 Aug 2019 21:33:17: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:33:17: #2 alternative fragment length(s) may be 4,119 bps INFO @ Mon, 12 Aug 2019 21:33:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05_model.r INFO @ Mon, 12 Aug 2019 21:33:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:33:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:33:17: #2 number of paired peaks: 547 WARNING @ Mon, 12 Aug 2019 21:33:17: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Mon, 12 Aug 2019 21:33:17: start model_add_line... INFO @ Mon, 12 Aug 2019 21:33:18: start X-correlation... INFO @ Mon, 12 Aug 2019 21:33:18: end of X-cor INFO @ Mon, 12 Aug 2019 21:33:18: #2 finished! INFO @ Mon, 12 Aug 2019 21:33:18: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:33:18: #2 alternative fragment length(s) may be 4,119 bps INFO @ Mon, 12 Aug 2019 21:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10_model.r INFO @ Mon, 12 Aug 2019 21:33:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:33:20: 28000000 INFO @ Mon, 12 Aug 2019 21:33:27: 29000000 INFO @ Mon, 12 Aug 2019 21:33:35: 30000000 INFO @ Mon, 12 Aug 2019 21:33:40: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:33:40: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:33:40: #1 total tags in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:33:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:33:41: #1 tags after filtering in treatment: 30594724 INFO @ Mon, 12 Aug 2019 21:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:33:41: #1 finished! INFO @ Mon, 12 Aug 2019 21:33:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:33:43: #2 number of paired peaks: 547 WARNING @ Mon, 12 Aug 2019 21:33:43: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Mon, 12 Aug 2019 21:33:43: start model_add_line... INFO @ Mon, 12 Aug 2019 21:33:44: start X-correlation... INFO @ Mon, 12 Aug 2019 21:33:44: end of X-cor INFO @ Mon, 12 Aug 2019 21:33:44: #2 finished! INFO @ Mon, 12 Aug 2019 21:33:44: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:33:44: #2 alternative fragment length(s) may be 4,119 bps INFO @ Mon, 12 Aug 2019 21:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20_model.r INFO @ Mon, 12 Aug 2019 21:33:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:34:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:34:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:35:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.05_summits.bed INFO @ Mon, 12 Aug 2019 21:35:06: Done! INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.10_summits.bed INFO @ Mon, 12 Aug 2019 21:35:06: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11771 records, 4 fields): 20 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6893 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:35:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981626/SRX3981626.20_summits.bed INFO @ Mon, 12 Aug 2019 21:35:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2667 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。